For the NES I'd go mainly with Dragon Warrior III and IV. I didn't get to play too many RPGs for the NES era, but a lot of people are suggesting the Ultima ports for the NES. In a way those are nicer than the PC originals since they have better graphics but due to the interface I'd still suggest playing them on the PC if you ever try an Ultima game. And they are worth trying, especially Ultima IV, VI, and VII (I know you can get VI on the SNES and I think you can get the first part of VII on the SNES but I'm not sure about that one).

For the Super NES, I agree with FF V and VI, Super Mario RPG, Chrono Trigger, and Battle Ogre. I'd also suggest Dragon Quest V, but you'll have to play a translated ROM for that though I think it's worth it as I'm a huge DQ fan and think V is one of the best in the series along with VIII. I really do recommend playing Earthbound though I'll say this: what makes Earthbound a memorable game isn't it's gameplay but damn near everything else about it.

Of course, whether or not that makes it a good game is debatable. But I will argue it is at least a wonderful experience.